Hi,
I am trying to assemble sequences using the phred,cross_match and phrap
softwares. I read the manuals and am a little bit confused on how to
use them.
I have 2 sequence files
1. abc_F.abi - forward read i.e read from 5' to 3' on the sense
strand and the other is,
2. abc_R.abi - reverse read i.e read from 5' to 3' on the antisense
strand.
I need to create a contig of these two sequences.
These are the following steps I performed.
1)
I used phred and created the following files
abc_F.abi.seq
abc_F.abi.qual
abc_R.abi.seq
abc_R.abi.qual
2) I used the following cross_match commands
cross_match abc_F.abi.seq vector -screen > screen.out
cross_match abc_R.abi.seq vector -screen > screen.out
where vector is the name of the sequence file of the vector in the
fasta format .
I got the following output files
abc_F.abi.seq.screen
abc_R.abi.seq.screen
3) I have confusion in using phrap.
My first doubt is how to assemble the above 2 sequences using phrap.
Should I write both the sequences in tht single file?
What should be the naming convention of the file?
Can I get a brief description on how to use phrap. the phrap
documentation is confusing and I am not able to understand.
Can anybody help me?
bye,
LT
